A while after Eggman's latest defeat, the doctor is still missing in action, and is presumed dead. The peace doesn't last very long, though, as Sonic receives a call from Tails explaining that Knuckles has been kidnapped by a mysterious new group named the Marauders, who have also stolen all the Chaos Emeralds. Sonic then teams up with Tails, Amy, and Rouge in order to rescue Knuckles. Things quickly spiral out of control, with a renewed Eggman (who seems to be on the side of good), the Marauder Army, and having to go to another dimension to retrieve the stolen Chaos Emeralds, where they will have to ally with other races they meet (and rescue), defeat the Dimension Lord Ix, and set things right once and for all.

Arson, Murder, and Admiration: After working together with Eggman, Tails seems to think of him less as an enemy and more as a fellow scientist, often commenting things like "Wow, I bet Eggman would love to see this!". If you call him out on it, he'll stop.

Animation Bump: Battles in the game run at 60FPS when it involves only two combatants. That gets cut in half(Or worse) when more combatants are added into the fray. One-on-one battles that pop up during the game end up invoking this as nearly all the battles in the game involve at least four fighters per side and thus miss out on the framerate boost. It helps that one-on-one battles in the game usually tend to be bosses.

A Taste of Power: Dr. Eggman has a lot of HP, a lot of PP and a ridiculously powerful and easy-to-execute special attack in Bombardment, as well as an instant kill attack against robots when used in conjunction with Tails. It's not a typical Taste of Power in that you don't start out with him, but he does leave the party about halfway through the game.

But Thou Must!: Averted. If you complete the (optional) quest of reuniting Cheese with Cream, she'll ask to join you on your quest. However if you refuse multiple times she will give up.

Chekhov's Boomerang: Emerl was picked up from Sonic Battle, dusted off, and woven into the Nocturnus' history.

Canon Discontinuity: Word of Saint Paul (arguably Word of Dante) stated "Sonic Chronicles is not canon. Or cannon. Or Ganon. Or Gammon. Or Jimmy Fallon." As for actual Word of God, for what it's worth, it firmly fits into the Sonic spinoff shelf as opposed to the "main line"note Mega Drive trilogy, Adventure, Adventure 2, Heroes, Unleashed, etc..

It's very unlikely that Sega will acknowledge the characters and story from this game ever again, since it would put them at risk for another lawsuit from Ken Penders.

Butt Monkey: One of the options the player has can make Shadow the butt of their joke.

Shadow: "I was going to beat them." Sonic: "Looks like the only one getting beaten around here is you!"

According to Word of God, the entire game was a Canon Immigrant, specifically of Knuckles' Archie Comics miniseries, hence all of the uncanny parallels between Shade, Imperatore Ix, and the Nocturnus to the comics' Julie-Su, Finitevus, and the Dark Legion. Ironically, this is probably the closest game you'll ever get based on the comics.

Continuity Nod: Several. The game is even helpful enough to provide you with a mini-encyclopedia on the previous Sonic games in one of the menus so you can get caught up on any of the relevant Backstory that you might not have played before or had forgotten about.

Expy: Shade is pretty clearly an expy of Julie-Su, and the Nocturnus are expies of the Dark Legion.

There's even an expied area with the Twilight Cage. Bioware admittedly just took Archie's echidna history and adapted it to the games, which got EVERYONE involved with the game in trouble when Ken Penders filed for copyrights to prevent this scenario happening again and Archie didn't address it before the copyrights kicked in.

Flanderization: Subverted for the majority of the cast, who have had their usual defining quirks diluted. Big the Cat however, usually just a mellow Ditz, is now a complete air head who speaks near solely in non sequiturs. You can also choose whether to do this or subvert it with Sonic's attitude.

In the backstory, it's shown that all of the Twilight Cage races were conquerors of some sort. When the Argus Event took them to the Twilight Cage, the Nocturnus conquered them and cruelly dominated them all. This had the somewhat positive effect of causing the other races to have a Heel Realization, since they saw the pain of being dominated.

Hypocrite: Imperator Ix accuses the other Twilight Cage races of being evil conquerors bent on controlling everything. This apparently makes it excusable for him to be an evil conqueror bent on controlling everything.

Immune to Mind Control: During the battle with the Voxai Overmind, there are four characters who are immune to his control. They are Sonic himself, E-123 Omega, Cream the Rabbit, and Big the Cat. Sonic is immune because he was in possession of a Great Emerald at the time, which gave him some protection, Omega because he's a robot, Big because he's The Ditz, and Cream because she's only six years old.

The Codex is filled with references to the Gizoid and the Fourth Great Civilization, which appear as plot points in Sonic Battle.

Amy uses Tarot cards, as per her original bio all the way back to Sonic CD.

You encounter Swatbots and roboticized animals.

Eggman makes a cute little allusion to Mean Bean Machine by talking about himself when he was "young and full of beans".

The game even does this on accident. One quest has the team deliver a young boy back to his home in Central City, but he refers to it as "Emerald Town", which was where Tails lived in Sonic Battle.

The whole concept of a still-living echidna race, exiled to the Twilight Cage, sounds like what the Archie Comics did with their echidna race first.

Never Say "Die": In the first few chapters, we get quotes like "we'll waste whatever time Knuckles has left" and "they wanted to get rid of me, but Shade ordered them to lock me up and keep me alive".

New Game+: Characters join your party at the same level they were at the end of the game. You're given the freedom to reassign all of their points used to boost their special abilities (except Sonic, since he technically never joins the party), allowing you to play around with new strategies. For some odd reason, although Chao Eggs regenerate, allowing you to collect any rare ones that you may have missed last time, rings don't, which means you have to depend on selling items back to the shops in order to make any more money.

Although, if you do a sidequest to free the animals from mind control, they will be replaced with repurposed Swatbots and other robots.

Obvious Beta: SEGA's contract with Bioware had just expired and they shifted their efforts to Dragon Age: Origins. As such, the game was released in a late beta stage, resulting in a bare-bones RPG with essentially no real sidequests. One of the most noticeable problems is the music and sound effects: most areas use placeholder Midi-format music of VERY low quality and pretty much all sound effects in battle are placeholder noises.

Odd Friendship: During Eggman's stint as a member of your party, he and Tails strike up a friendship.

One-Hit Kill: Spartoi, a special Chao, allows for a random chance to oneshot an opponent regardless of armor when the character he's with attacks.

One-Hit-Point Wonder: Built on the "Shedinja" model. Super Sonic and Super Imperator Ix both do massive damage with each blow, but if they don't take out their opponent in one turn (by not executing the Action Commands perfectly for Sonic, or by the player screwing up enough Action Commands for Ix), their health regenerates and they have to start over.

Operation: Jealousy: Amy claims to have a new boyfriend named Dexter. He's never seen, and depending on dialogue choices, Sonic suspects she's making him up. If you're nice to Amy throughout the game, she eventually admits that she made him up.

Point of No Return: Multiple. Whatever you do, make absolutely sure you follow Eggman's advice and don't go into Metropolis unless you're sure you've got everything you need. Also, make sure to get everything in Metropolis before trying to recapture the Master Emerald. And after that, get everything in Metropolis Ground Zero before finishing the chapter, and then make sure you have everything from the Twilight Cage before starting chapter 10.

Poor Communication Kills: When the heroes attempt to track down Eggman using a device, they end up finding Shadow in Mystic Ruins. But rather than tell them why he was there (Finding Omega), he instead picks a fight with Sonic when he feels they're accusing him of something. And when they meet him again, he tries to run away from them and has to be beaten by Sonic again to get him to talk with them.

Precursors: Someone lived in the Twilight Cage before anyone else did, and Nestor calls them this.

Randomly Drops: Chao are obtained at random each time you get an egg. You could get all the best ones right off the bat or end up with crappy ones throughout the course of the game. Somewhat helped by the ability to trade chao with friends.

However, the randomness of the chao can be exploited by saving before checking the egg. Different chao are hatched every time you load the same save and check the egg.

Villain Ball: Way to announce your plans for world conquest right in front of your lieutenant who believed you wanted to simply return to Earth, Ix.

Well-Intentioned Extremist: Shade knows what she does under Ix is wrong, but views it as necessary to escape the Cage. Once she realizes Ix was using the Nocturnus to fuel his bid for conquest, she promptly defects from him.

World of Snark: You know it's this when even Big the Cat gets in on it.

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